Appendix C. Commands on one page
Everything you can ask an AI to do can also be done with the commands below. Use them in a terminal (Command Prompt or PowerShell on Windows, Terminal on macOS and Linux, or the terminal inside an editor) while in the repository folder. First switch the environment on (conda activate fig-atlas, from any folder).
- Every command explains itself with
fa --help and fa <command> --help.
- Add
--dry-run to a command that changes files and it only shows what would change, writing nothing.
- Add
--json and the result comes in a format for programs (the way an AI uses it).
Projects and data
| You want to |
Command |
Chapter |
| Create a project |
fa new project name --domain lab --category exploratory |
4 |
| Check a bundle |
fa bundle check bundle-folder |
3 |
| See the kinds of figure and their contracts |
fa bundle contracts |
3 |
| Attach a bundle as a panel (+ build) |
fa ingest bundle bundle-folder --project name |
4 |
| List projects |
fa list |
— |
| See the names of figures that can be drawn |
fa renderers |
— |
Building and checking
| You want to |
Command |
Chapter |
| Build |
fa build name |
4 |
| Build + preflight |
fa build name --preflight |
8 |
| Verify only |
fa verify name |
8 |
| See where a config value comes from |
fa param explain name plots.panel.key |
6 |
| Write into the config the keys a build took from defaults |
fa param sync name (preview) → --apply |
6 |
| Find unused config keys and typos |
fa lint name |
6 |
| Find hand-typed numbers |
fa claims name --list |
9 |
| Audit printed sizes |
fa audit-print |
7 |
Provenance and freshness
| You want to |
Command |
Chapter |
| Find stale figures |
fa status |
10 |
| Figures that use this file |
fa impact file-path |
10 |
| A figure's sources |
fa lineage name |
10 |
| What changed since a snapshot |
fa diff-figure name |
10 |
| A package for submission (RO-Crate zip) |
fa export name --zip |
7 |
A paper's life and the storyline
| You want to |
Command |
Chapter |
| Promote |
fa promote name --figure 2 --slug short-name |
11 |
| Retire |
fa retire name |
11 |
| Rewrite the mapping table |
fa storyline registry |
11 |
| Check the storyline's consistency |
fa storyline check |
11 |
| Draft what changed |
fa storyline diff --draft |
11 |
| Sync the revision records |
fa storyline revisions --sync |
11 |
| Compendium PDF (strict; also saves this point's snapshot) |
fa storyline compile --strict |
11 |
| Save the record of what changed |
fa storyline diff --write |
11 |
| List the saved snapshots |
fa storyline snapshots |
11 |
| Trace a figure's evidence |
fa storyline evidence "Main Figure 3" |
11 |
For people who build things
| You want to |
Command |
| Start a new kind of figure (a renderer) |
fa new renderer name --plot-type kind |
| Check for numbers typed into code |
fa lint --hardcoded |
| Offer the tools to an AI assistant |
fa mcp (how to connect) |
Run fa new renderer in a research repository and the renderer is made in that repository's renderers/ folder. Without installing or changing the package, fa renderers, fa ingest bundle and fa build find that renderer, and the provenance record keeps its file too. If the shape would serve other research as well (bars, lines, scatter, heatmaps), consider moving it into the fig-atlas core later.
Previous: Appendix B. Questions and troubleshooting · Next: Appendix D. Further reading